rs11046688

Variant names:

• chr12-22922420-G-A
• rs11046688
• ENST00000538317.6:n.308+34376G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000538317.6(LINC02955):​n.308+34376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,118 control chromosomes in the GnomAD database, including 3,854 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3854 hom., cov: 32)
• Consequence: LINC02955 ENST00000538317.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 3 publications found

Genes affected

LINC02955 (HGNC:55973): (long intergenic non-protein coding RNA 2955)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02955	NR_187500.1	n.566+34376G>A		intron_variant	Intron 4 of 11
LINC02955	NR_187501.1	n.410+34376G>A		intron_variant	Intron 3 of 11
LINC02955	NR_187503.1	n.634+34376G>A		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02955	ENST00000538317.6	n.308+34376G>A		intron_variant	Intron 3 of 11	4

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30264 AN: 152000 Hom.: 3854 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.207

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.199 AC: 30266 AN: 152118 Hom.: 3854 Cov.: 32 AF XY: 0.199 AC XY: 14803 AN XY: 74352

African (AFR) AF: 0.0493 AC: 2048 AN: 41526

American (AMR) AF: 0.201 AC: 3072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1088 AN: 5166

South Asian (SAS) AF: 0.0851 AC: 410 AN: 4820

European-Finnish (FIN) AF: 0.354 AC: 3737 AN: 10562

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18752 AN: 67970

Other (OTH) AF: 0.206 AC: 436 AN: 2114

Alfa AF: 0.243 Hom.: 6134

Bravo AF: 0.184

Asia WGS AF: 0.124 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.51
PhyloP100		-0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11046688; hg19: chr12-23075354;